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The present study assessed the prevalence of infectious agents in Litopenaeus vannamei culture systems (intensive, semi-intensive, and extensive) on farms located in Tamaulipas, Mexico. We also analyzed the statistical relationship between these agents and the physicochemical parameters related to the aquatic environment during the summer-autumn of 2008 and the spring–summer of 2009. Acineta sp. at the Reynosa farm, showed a significant correlation with temperature and was the only protozoan found at this farm, which uses semi-intensive culturing with underground water, and showed the best conditions related to lower impacts of infectious diseases. La Pesca shrimp farm uses water from the Laguna Madre estuary and an extensive culture system. Epistylis sp. at the La Pesca farm and the Moron farm showed a significant relationship with turbidity; the dependence of Nematopsis sp. on temperature at La Pesca was highly significant. The filamentous bacterium, Leucothrix mucor , was found at the Moron farm, which uses an intensive production system with freshwater from the Tigre River. To our knowledge, this report is the first to analyze the relationship of this filamentous bacterium with water quality. These results could provide important information for future epidemiological studies to facilitate better resource management and the prevention of infectious or parasitic diseases in farmed shrimp.