In addition to anthropogenic mechanisms of dispersal, establishment of round goby, Neogobius melanostomus, in the Laurentian Great Lakes has generally benefitted from continuous connections among the lakes and accessible shorelines. This dissertation (1) examined the effects of distance in affecting round goby invasion and the native pumpkinseed sunfish Lepomis gibbosus population along the lake shoreline as reflected by morphological differences, (2) estimated the co-occupancy of round goby and native benthic fish (i.e. darters) in the tributary system and (3) analyzed the impact on population genetics resulting from round goby invasion in streams as inferred from gene flow. The study area spanned the Lake Ontario shoreline and its tributaries in the northwestern area of New York. Morphological variation was found to be significantly different among sampled sites for pumpkinseed, but was not found to be significant for round goby. For pumpkinseed, samples from river-mouth sites showed shallower body depth than that of samples from bay-area sites. The degree of morphological variation for pumpkinseed increased with distance but the effect was not significant for round goby. The study further showed when estimating species occurrence using presence/absence data, models that assumed perfect detection (p = 1) when round goby are present can be underestimated as much as 5 to 60% as compared to models that assumed imperfect detection (p < 1) when the probability of occupancy of darters was considered. While the occupancy of streams by round goby decreased with link magnitude (a proxy for stream size), the probability of occupancy by round goby can also be underestimated by 2 to 15% when imperfect detection is not accounted for. Lastly, I found population genetic differentiation of round goby at fine scales, where individuals collected in the invaded areas exhibited at least two distinct lineage clusters that predictably coincided with the closest major waterways, Lake Ontario and the Erie Canal. Also the round goby population did not exhibit signs of founder effects with respect to stream network structure in the study area. In conclusion, identification of the differential response in body-shape morphology suggests that localized threat on limited-dispersal species like pumpkinseed by invasive generalist species like round goby could affect selection. Where habitat heterogeneity contributes little to no impact on round goby colonization, estimation of colonization and impacts on native benthic fish in the invaded areas should account for imperfect detection of sampling. Information from this study can be adapted to develop early invasive species detection in developing control management of further invasion and for conservation of native species.