When onsite wastewater treatment and disposal systems (OSTDS) are not sited appropriately or installed properly, wastewater constituents can be a source of adverse environmental impacts to soil and groundwater, which can lead to potential public health risks. A paired monitoring design developed to compare water quality in sewered and non-sewered areas is presented here. It is suggested as a possible monitoring scheme for assessing the impact of sewer installation projects. As such, two sets of single-family, rural residential Florida neighborhoods were evaluated over a two-year period to gain insight into the effects of small-community use of OSTDS on coastal water quality. One set of two neighborhoods were connected to the sanitary sewer network and the other set of two were served exclusively by OSTDS. Water quality sampling was conducted at the paired sites during seasonal high water table (SHWT) and seasonal low water table (SLWT) events. Measured surface water quality during the SHWT showed indications of environmental impacts from OSTDS in terms of nutrients, microbial pathogen indicators, and other water quality measures, such as turbidity and conductivity. However, during the SLWT events, no obvious impacts attributable to OSTDS were detected. The water quality results indicate that OSTDS impacts may be measureable in rural areas. Other factors, such as microbial indicator survival and regrowth potential, may confound the understanding of water quality impacts of sewer projects. For example, the microbial indicators Escherichia coli and enterococci were found to persist over time and therefore did not always represent true comparisons of OSTDS and sewered areas between seasons. The timeframe for evaluating the effects of sewer projects may be longer than anticipated because of this survival and regrowth phenomenon.