Mosquito management in wetlands is complex partly because some of the wetland management operations are known to enhance mosquito production. I aimed to describe the effects of nutrients and integrated mosquito management strategies on mosquitoes produced in wetlands in the following three studies. First, we evaluated the growth characteristics of alkali bulrush (Schoenoplectus maritimus), an alternative aquatic plant of potential bioremediation importance, and its associated mosquito production across a gradient of nitrogen enrichment including the high ammonium nitrogen regimens typically found in constructed wetlands. Mosquito larvae abundance, dominated by the western encephalitis mosquito (Culex tarsalis Coquillett), was significantly greater in enriched versus unenriched mesocosms. Alkali bulrush survived high nitrogen loadings, but its biomass was significantly suppressed at high (>50 mg/liter) ammonium nitrogen concentration in the water. Second, we characterized microbiota associated with C. tarsalis larvae, water column and epibionts of two (alkali and California) bulrushes using 16S rRNA gene sequences generated with Illumina sequencing platform. The diversity of microbiota in mosquitoes sampled from wetlands containing the two bulrushes did not differ appreciably, and was chiefly dominated by Thorsellia (Gammaproteobacteria). The epibionts of the bulrushes and bacterioplankton were dominated by members of Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria and Verrucomicrobia. Overall, nearly 49% of the Bacteria taxa found in the mosquito gut were also found in the habitat, suggesting a strong Culex larvae-Bacteria interaction. Finally, we evaluated the effects of a one-time application of two rates of a key mosquito biopesticide, Bacillus thuringiensis subsp. israelensis (a granular form of VectoBac G) on native microbiota and physicochemical variables in the feeding zone of Culex larvae in experimental mesocosms. Beta diversity of Bacteria communities revealed that samples from low Bti and untreated control mesocosms were significantly separated from high Bti mesocosms and were dominated by unidentified OTU of Cyanobacteria, Cytophagales and Cyclobacteriaceae (Bacteroidetes), and Sphingomonas (Alphaproteobacteria). Phytoplankton (chlorophyll a), sestonic particulates, nutrients, pH and other physicochemical variables in the water column were also significantly reduced in the high Bti mesocosms. Important implications of the results of these studies on integrated mosquito management in aquatic ecosystems are discussed.