Climate change and pollution are threatening inland freshwater ecosystems which contribute to human well-being by providing food and incomes. To address this issue, aquaculture is expanding sometimes in intensive settings. We aimed to assess the nutritional and contaminant profiles of three fish species (Channa micropeltes, Pangasianodon hypophthalmus, Clarias microcephalus) from the wild ecosystem and caged culture in the Tonle Sap Lake. The mineral profile was assessed by ICP-MS and the overall nutritional quality was characterized by SAIN-LIM scores. Using data on fish consumption by pregnant women, we estimated the daily intakes of several potentially toxic elements. Overall, fish species had similar nutritional profiles, regardless of production method. Only lipid content was higher in caged systems. The production method had no influence on mineral profile and potentially toxic element contents except for mercury higher among wild Pangasianodon hypophthalmus (2.1¿µg/100¿g). With a consumption of 108¿g of fish per day per woman, the median estimated daily intakes of potentially toxic elements were below the tolerable daily limits. However, three women who ate large quantities of fish had mercury intakes (30–32¿µg/day) that exceeded the tolerable daily intake. When the rice consumption was taken into account, a high number of women had inorganic arsenic intakes (20–80¿µg/day) exceeding the tolerable daily limits. This work is a contribution to the assessment of the risks of arsenic and mercury exposure for pregnant women in Cambodia integrating real food consumption data.