Accumulations of agricultural chemicals and sediment in lakes may affect mosquito populations and their associated risks of disease. We compared physical, chemical and biological attributes for two lakes in northeastern Iowa to identify correlates with numbers of immature mosquitoes. Although we identified significant differences between lakes and among years, most attributes were also highly variable within lakes and within years. Maps representing temporal and spatial heterogeneity are presented for open water transects and shoreline sample sites monitored during the study. Silver Lake (Delaware County, IA), with a greater proportion of its watershed used for agriculture, had higher open water chlorophyll a and total phosphorous levels than Casey Lake (Tama County, IA). Likewise, densities of bacteria at Silver Lake shorelines sites were also significantly greater during the period of study (1999 – 2001). Casey Lake produced significantly more non-culicid insects than Silver Lake, thereby supporting a greater diversity of fish. Likewise, recreational use for Casey Lake was much greater than for the more polluted lake. However, both lakes were highly impacted and we found no difference in overall numbers of mosquito larvae and pupae using the most rigorous statistical tests necessitated by high levels of variation. Only shoreline vegetation consistently covaried with mosquito numbers for the lakes. Although it had significantly greater inundated shoreline vegetation, Silver Lake did not support significantly more mosquito larvae and pupae. Nonetheless, the mosquito species developing in Silver Lake may pose greater risks of disease transmission than the species in Casey Lake.