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28. Jahnsen-Guzmán, N.; Lagos, N.A.; Lardies, M.A.; Vargas,A.; Fernández, C.; San Martín, V.A.; Saavedra, L.M.; Cuevas, L.A.; Quijón, P.A.; Duarte, C. (2021) Environmental refuges increase performance of juvenile mussels Mytilus chilensis: Implications for mussel seedling and farming strategies. Science of the Total Environment 751. https://doi.org/10.1016/j.scitotenv.2020.141723
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31. Riquelme-Bugeño, R.; Pérez-Santos, I.; Alegría, N.; Vargas, C.A.; Urbina, M.A. & Escribano, R. (2020)  Diel vertical migration into anoxic and high pCO₂waters: Acoustic and net based krill observations in the Humboldt Current System. Nature Scientific Reports. 10,17181. https://doi.org/10.1038/s41598-020-73702-z
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33. Saavedra, L.M.; Saldías, G.S.; Broitman, B.R.; Vargas,C.A. (2020) Carbonate Chemistry Dynamics in Shellfish Farming Areas along the Chilean coast: Natural Ranges and Biological implications. ICES Journal of Marine Sciences.https://doi.org/10.1093/icesjms/fsaa127
34. Vargas, C.A.; Garreaud, R.; Barra, R.; Vásquez-Lavín, F.; Saldías, G.S.; Parra O. (2020) Environmental costs of water transfers. Nature Sustaintability4, https://doi.org/10.1038/s41893-020-0526-5
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37. Vergara-Jara, M.J.; DeGrandpre, M.D.; Torres, R.; Beatty, C.M.; Cuevas, L.A.; Alarcón, E.; Iriarte, J.L. (2019) Seasonal changes in carbonate saturation state and air-sea CO₂fluxes during an annual cycle in a stratified-temperate fjord (Reloncaví Fjord, Chilean Patagonia). Journal of Geophysical Research: Biogeosciences 124 (9): 2851-2865. https://doi.org/10.1029/2019JG005028
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45. Saavedra, L.M.; Parra, D.; San Martín, V.; Lagos, N.A.; Vargas, C.A.(2018) Local habitat influences on feeding and metabolic performance upon high pCO₂levels of the intertidal mussels Perumytilius purpuratus. Estuaries and Coasts 41(4): 1118 – 1129. https://doi.org/10.1007/s12237-017-0333-z
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48. Iriarte, J.L.; Cuevas, L.A.; Cornejo, F. Silva, N.; González, H.E.; Castro, L.; Montero, P.; Vargas, C.A.;Daneri, G. (2018) Low spring primary production and microplankton carbon biomass in Sub-Antarctic Patagonian channels and fjords (50-53ºS). Artic, Antarctic, and Alpine Research50(1): e1525186. https://doi.org/10.1080/15230430.2018.1525186
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50. Jacob, B.G.; Von Dassow, P.; Salisbury, J.E.; Navarro, J.M.; Vargas, C.A.(2017) Impact of low pH/high pCO2 on the physiological response and fatty acid content in diatom Skeletonema pseudocostatum. Journal of The Marine Biological Association of United Kingdom,97(1): 125 – 133. https://doi.org/10.1017/S0025315416001570
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68. Duarte, C.H.; Navarro, J.M.; Acuña, K.; Torres, R.; Manríquez, P.H.; Lardies, M.; Vargas, C.A.;Lagos, N.A.; Aguilera, V. (2014) Combined effects of temperature and Ocean acidification on the juvenile individuals of the mussel Mytilus chilensis. Journal of Sea Research 85: 308-314. https://doi.org/10.1016/j.seares.2013.06.002
69. Lardies M.A., Arias M.B., Poupin M.J., Manríquez P.H., Torres R., Vargas C.A.,Navarro J.M. & Lagos N.A. (2014) Differential response to ocean acidification in physiological traits of Concholepas concholepasJournal of Sea Research, 90: 127-134. https://doi.org/10.1016/j.seares.2014.03.010
70. Manríquez, P.H.; Jara, M.E.; Mardones, M.L.; Torres, R.; Navarro, J.M.; Lardies, M.A.; Vargas, C.A.; Duarte, C.; Lagos, N.A. (2014) Ocean acidification affects predator avoidance behavior but not prey detection in the early ontogeny of a keystone species. Marine Ecology Progress Series 502: 157-167.https://doi.org/10.3354/meps10703
71. Silva N. & Vargas, C.A. (2014) Hypoxia in Chilean Patagonian Fjords. Progress in Oceanography, 129: 62 – 74. https://doi.org/10.1016/j.pocean.2014.05.016
72. Lafon, A.; Silva, N.; Vargas, C.A. (2014) Contribution of allochthonous organic carbon across the Serrano River Basin and the adjacent fjord system in Southern Chilean Patagonia: insights from the combined use of stable isotope and fatty acid biomarkers. Progress in Oceanography. 129: 98 – 113. https://doi.org/10.1016/j.pocean.2014.03.004
73. Manríquez, P.H.; Jara, M.E.; Mardones, M.L.; Torres, R.; Lagos, N.A.; Lardies, M.A. Vargas, C.A.; Duarte, C. & Navarro, J.M. (2014) Effects of ocean acidification on developing and early post hatching larval traits of Concholepas concholepas(loco). Marine Ecology Progress Series 514: 87-103. https://doi.org/10.3354/meps10951
74. Navarro, J.M.; Torres, R.; Acuña, K.; Duarte, C.; Manríquez, P.H.; Lardies, M.; Lagos, N.A.; Vargas, C.A.; Aguilera, V. (2013) Impact of medium-term exposure to elevated pCO₂levels on the physiological energetics of the mussel Mytilus chilensis. Chemosphere 90: 1242–1248.https://doi.org/10.1016/j.chemosphere.2012.09.063
75. Vargas, C.A.; Arriagada, N.L.; Sobarzo, M.; Contreras, P.Y.; Saldías, G. (2013) Bacterial production across a river to ocean continuum in Central Chile: Implications for organic carbon cycling. Aquatic Microbial Ecology68: 195–213. https://doi.org/10.3354/ame01608
76. Aguilera, V.M.; Vargas, C.A.; Manríquez, P.H.; Navarro, J.M.; Duarte, C. (2013) Low-pH Freshwater Discharges Drive Spatial and Temporal Variations in Life History Traits of Neritic Copepod Acartia tonsa. Estuaries and Coasts 36: 1084 – 1092. https://doi.org/10.1007/s12237-013-9615-2
77. Vargas, C.A.;De La Hoz, M.; Aguilera, V.; San Martin, V.; Manríquez, P.H.; Navarro, J.M.; Torres, R.; Lardies, M.A.; Lagos, N. (2013) CO2-driven ocean acidification reduces larval feeding efficiency and change food selectivity in the mollusk Concholepas concholepas. Journal of Plankton Research35(5): 1059 – 1068. https://doi.org/10.1093/plankt/fbt045
78. Manríquez, P.H.; Jara, M.E.; Mardones, L.; Navarro, J.M.; Torres, R.; Lardies, M.A.; Vargas, C.A.Duarte, C.; Widdicombe, S.; Salisbury, J.; Lagos, N.A. (2013) Ocean acidification affects prey-predator interactions but not net prey shell growth. PLoS ONE 8(7): e68643. https://doi.org/10.1371/journal.pone.0068643
79. González, H.E.; Castro, L.; Daneri, G.; Iriarte, J.L.; Silva, N.; Tapia, F.; Teca, E.; Vargas, C.A.(2013) Land-ocean gradient in haline stratification and its effects on plankton dynamics and trophic carbon fluxes in Chilean Patagonian fjords (47° – 50°S). Progress in Oceanograph 119: 32 – 47.
80. Torres, R.; Manríquez, P.H.; Duarte, C.; Navarro, J.M.; Lagos, N.A.; Vargas, C.A.& Lardies, M.A. (2013) Evaluation of  a semi-automatic system for long-term seawater carbonate chemistry manipulation. Revista Chilena de Historia Natural 86: 443 – 451.
81. Iriarte, J.L.¸Vargas, C.A.; Bermúdez, R.; Urrutia, R.E.; Tapia, F.J. (2012) Primary production and plankton carbon biomass in a river-influenced upwelling area off Concepción, Chile. Progress in Oceanography92(1): 97-109
82. Vargas, C.A.; Contreras, P.Y.; Iriarte J.L. (2012) Relative importance of phototrophic, heterotrophic, and mixotrophic nanoflagellates in the microbial food web dynamic of a river-influenced coastal upwelling area. Aquatic Microbial Ecology 65: 233 – 248.
83. Léniz, B.; Vargas, C.A.; Ahumada, R. (2012) Characterization and comparison of microphytoplankton biomass in the lower reaches of the Biobío River and the adjacent coastal area off Central Chile during autumn-winter conditions. Latin American Journal of Aquatic Research 40(4) 847 – 857.
84. Vargas, C.A.;Martínez, R.A.; San Martín, V.; Aguayo, M.; Silva, N.; Torres, R. (2011) Allocthonous subsidies of organic matter across a lake-river-fjord landscape in the Chilean Patagonia: Implications for marine plankton food webs. Continental Shelf Research, 31: 187 – 201
85. Czypionka, T.; Vargas C.A.;Silva, N.; Daneri, G.; González, H.E.; Iriarte, J.L. (2010) Importance of mixotrophic nanoplankton in the fjord region of southern Chile. Continental Shelf Research, 31: 216 – 224
86. González, H.E.; Castro, L.; Daneri, G.; Iriarte, J.L.; Silva, N.; Vargas, C.A.; Giesecke, R.; Sánchez, N. (2011) Seasonal plankton variability in Chilean Patagonia Fjords: carbon flow through the pelagic food web of the Aysen Fjord and plankton dynamics in the Moraleda Channel basin. Continental Shelf Research, 31: 225 – 243
87. Silva, N.; Vargas, C.A.; Prego, R. (2011) Land-ocean distribution of allochthonous organic matter in the surface sediments of the Chiloé and Aysén interior seas (Chilean Northern Patagonia). Continental Shelf Research, 31: 330 – 339
88. González, H.E.; Calderón, M.J.; Castro, L.; Clement A.; Cuevas, L.A.; Daneri, G.; Iriarte, J.L.; Lizárraga, L.; Martínez, R.; Menschel, E.; Silva, N.; Carrasco, C.; Valenzuela, C.; Vargas, C.A. & Molinet C. (2010) Primary production and plankton dynamics in the Reloncaví Fjord and the Interior Sea of Chiloé, Northern Patagonia, Chile. Marine Ecology Progress Series 402: 13 – 30.
89. Vargas, C.A.; Martínez, R.A.; Escribano, R.; & Lagos N.A. (2010) The relative influence of food quantity, quality, and selectivity on zooplankton growth regulation in coastal food webs. Journal of Marine Biological Association of United Kingdom90(6): 1189 – 1201.
90. Vargas, C.A.& Martínez, R.A.(2009) Grazing impact in natural populations of ciliates and dinoflagellates over a river-influenced continental shelf. Aquatic Microbial Ecology 56: 93 – 108 
91. Vargas, C.A.;A. Martínez& H. E. González (2008) Contrasting trophic interactions in microbial and copepods communities in a fjord ecosystem (Chilean Patagonia). Aquatic Microbial Ecology, 53: 227 – 242.
92. Vargas, C.A.;Cuevas, A.; González, H.E. & Daneri, G. (2007) Bacterial growth response to copepod grazing in aquatic ecosystems. Journal of Marine Biological Association of United Kingdom 87: 667 – 674.
93. Vargas, C.A.;Martínez, R.; Cuevas, L.A.;Pavez, M.A.; Cartes, C.; González, H.E.; Escribano R & Daneri, G. (2007). The relative importance of microbial and classical food webs in a highly productive coastal upwelling area. Limnology & Oceanography 52 (4): 1495 – 1510.
94. Thiel, M.; Macaya, E.; Acuña, E.; Arntz, W.; Bastias, H.; Brokordt, K.; Camus, P.; Castilla, J.C.; Castro, L.R.; Cortés, M.; Dumont, C.P.; Escribano, R.; Fernández, M.; Lancelloti, D.; Gajardo, J.A.; Gaymer, C.F.; Gomez, I.; González, A.E.; González, H.E.; Haye, P.A.; Illanes, J.-E.;Iriarte, J.L.; Luna-Jorquera, G.; Luxoro, C.; Manr´ñiquez, P.H.; Marín, V.; Muñoz, P.; Navarrete, S.A.; Pérez, E.; Poulin, E.; Sellanes, J.; Sepúlveda, A.; Stotz, W.; Tala, F.; Thomas, A.; Vargas , C.A.; Vásquez, J.A. & Vega, A. (2007) The Humboldt Current System of Northern and Central Chile: Oceanographic Processes, Ecological Interactions and Socio-Economic Feedback. In: Oceanography and Marine Biology – An Annual Review45: 195 – 344.
95. Poulet, S.A.; Escribano, R.; Hidalgo, P.; Cueff, A.; Wichard, T.; Aguilera, V.; Vargas, C.A.& Pohnert, G. (2007) Collapse of Calanus chilensisreproduction in a marine environment with high diatom concentration. Journal of Experimental Biology and Ecology 352: 187 – 199.
96. Vargas, C.A.; P. Manríquez & S.A. Navarrete (2006) Feeding by larvae of intertidal invertebrates: assessing their position in pelagic trophic webs. ECOLOGY87 (2): 444 – 457.
97. Narváez D.; S.A. Navarrete; J Largier & Vargas, C.A(2006) Onshore advection of warm water and larval invertebrate settlement during relaxation of upwelling off central Chile. Marine Ecology Progress Series309: 159 – 173.
98. Vargas, C.A.; Narváez; Piñones A.; S.A. Navarrete & N. Lagos (2006) Larval transport of barnacles influenced by the dynamic of a river plume. Journal of Marine Biological Association of United Kingdom86: 1057 – 1065.
99. Vargas, C.A.; Escribano, R. & Poulet, S. (2006) Phytoplankton diversity determines time-windows for successful zooplankton reproductive pulses. ECOLOGY87 (12): 2992 – 2999. 
100. Piñones, A.; A. Valle-Levinson; D. Narváez; A. Vargas; S. Navarrete & J. C. Castilla (2005) Wind-induced diurnal variability in river plume motion. Estuarine, Coastal & Shelf Science, 65: 513-525.
101. Tönnesson, K.; M. Maar; A. Vargas; E.F. Møller; S. Satapoomin; S. Zervoudaki; E. Christou; A. Giannakourou; A. Sell; J.K. Petersen; T.G. Nielsen & P. Tiselius (2005) Grazing impact of Oikopleura dioicaand copepods on an autumn plankton community. Marine Biology Research1 (5): 365 – 373.
102. Vargas, C.A.; D. Narváez; A. Piñones, R. Venegas & S.A. Navarrete (2004) Internal tidal bore warm fronts and settlement of invertebrates in central Chile. Estuarine, Coastal & Shelf Science, 61: 603 – 612
103. Vargas, C.A.& H. González (2004) Plankton Community Structure and Carbon Cycling in a Coastal Upwelling System (I): Contribution of Bacteria, Ciliated Microprotozoans and Dinoflagellates to the diet of Copepods and Appendicularians. Aquatic Microbial Ecology 34: 151 – 164
104. Vargas, C.A.& H. González (2004) Plankton Community Structure and Carbon Cycling in a Coastal Upwelling System (II): Microheterotrophic pathway. Aquatic Microbial Ecology34: 165 – 180
105. González, H.E.; R. Giesecke; A. Vargas; M. Pavéz; J.L. Iriarte; P. Santibañez; L. Castro; R. Escribano & F. Pagés (2004) Carbon cycling through the pelagic food web in the northern Humboldt Current off Chile (23 °S). ICES Journal of Marine Science 61 (4): 572 – 584
106. Vargas, C.A. & L.P. Madin (2004) Zooplankton feeding ecology: Clearance and ingestion rates of the salps Thalia democratica, Salpa cylindrica andCyclosalpa affinison naturally occurring particles in the Mid-Atlantic Bight. Journal of Plankton Research 26 (7): 827 – 833
107. Vargas, C.A.; S. Araneda & G. Valenzuela (2003) Influence of tidal phase and circulation on larval fish distribution in a partially mixed estuary, Corral Bay, Chile. Journal of the Marine Biological Association of the United Kingdom83: 217 – 222
108. Tiselius, P.; J.K. Petersen; T.G. Nielsen; M. Maar; E.F. Møller; S. Satapoomin; K Tönnesson; T Zervoudaki; E. Christou; A. Giannakourou; A. Sell & Vargas, C.A.(2003). Functional response of Oikopleura dioicaand house clogging due to exposure to algae of different size. Marine Biology 142: 253 – 261
109. Valenzuela, G. & Vargas, C.A.(2002) Comparative larval growth rate of Sprattus sprattusin relation to biological and oceanographic features in the North Sea. Archive of Fisheries and Marine Research 49 (3): 213 – 230
110. Vargas, C.A.; K. Tönnesson; M. Maar; E.F. Møller; S. Satapoomin; T. Zervoudaki; E. Christou; A. Giannakourou; A. Sell & P. Tiselius (2002) Importance of copepods versus appendicularians in vertical carbon fluxes in a Swedish fjord. Marine Ecology Progress Series241: 125 – 138
111. Vargas, C.A.& L. Castro (2001) Spawning of the Chilean hake (Merluccius gayi gayi) in the upwelling system off central-southern Chile in relation to oceanographic and biological features. Scientia Marina65 (2): 101 – 110
112. Vargas, C.A.; G. Valenzuela; S. Núñez & D. F. Arcos (1997) Role of oceanographic and topographic factors in the retention of hake (Merluccius gayi gayi Guichenot 1848) larvae in the upwelling system off central-southern Chile. Archive of Fisheries and Marine Research 45 (3): 201 – 222
113. Vargas, C.A.; G. Valenzuela; S. Núñez & D. F. Arcos (1996) Natural mortality of hake larvae (Merluccius gayi gayi) off Central-southern Chile in relation to their spatial distribution and patchiness. Investigaciones Marinas, 24: 19 – 30