Shellfish beds in the Chesapeake Bay region are being contaminated with fecal coliform bacteria which can cause the beds to be closed to harvesting. The cause of the bacteria contamination is basically unknown but has been hypothesized to be coming from non-point sources of pollution. The suggested source of the bacteria is on-site waste disposal systems (OSWDS) including septic tanks. Septic tank effluent (STE) may be transported through the soil and contaminate the groundwater. Submarine groundwater discharge (SGWD) may then be providing a conduit into the estuary for the bacteria. Data of OSWDS locations was not available, thus the groundwater transport mechanism was the focus of the study. A comprehensive analysis was performed on fecal coliform concentration measurements taken from 1981 through 1992 in the Chesapeake Bay region. In all, over 191,000 bacteria concentration measurements in the main database were considered. An analysis of various hydrological factors was made to determine how much these factors affected the bacteria most probable number (MPN) concentration levels. Subsets of the data consisting of heavy rain events, low tide and high tide were analyzed which had geometric mean bacteria MPN concentrations of 16.1 fecal coliforms (FC) / 100 mL, 9.4 FC / 100 mL, and 6.9 FC / 100 mL respectively compared to an overall geometric mean of 7.8 FC / 100 mL. Of the factors analyzed, rain events and tidal elevation had the most affect on bacteria MPN levels. Other factors analyzed were secchi depth, salinity, season, and water temperature. Additional data was available for Virginia's Eastern Shore including soil permeability, hydraulic gradient and land use which allowed for a more detailed analysis of samples taken in this area. A multiple regression correlation on bacteria MPN measurements with water quality data of the Eastern Shore yielded an R* value of 22.2% which does not statistically link groundwater transport and high bacteria counts. Many factors, which were calculated using a geographic information system (GIS), were examined, including near shore soil permeability, season, and surface area of water within a 400 meter radius, to determine their contribution to high area of water within a 400 meter radius, to determine their contribution to high bacteria concentration measurements. The factors used in the multiple regression were near shore soil permeability, near shore soil Darcy velocity, near shore soil hydraulic gradient, proximity to shoreline, proximity to wastewater treatment plant, rain in the last two days prior to sample collection, runoff event occurrence, salinity, season, urban land use, agricultural land use, pasture land use, surface area of water in a 400 meter radius, tide elevation, and water temperature. Of these factors, distance upstream, rain, tide and season were determined to have the highest effect on geometric mean bacteria concentrations. Groundwater transport could not be statistically linked to high bacteria MPN counts. Thus OSWDS can not be linked as the source of the contamination. Further research on a more local basis is necessary to examine the relationship between OSWDS usage and bacteria MPN levels. A GIS proved to be a very important tool for examining the effects of the different data sets. / Master of Science