Movement and dispersal patterns are key biological processes across a range of organisational levels. The Fundulus notatus species complex includes several species with similar ecological niches that exhibit broadly overlapping ranges. We conducted a mark–recapture study on two of the most widely distributed members of this species complex to improve our understanding of their movement and habitat use. A population of F. notatus was studied between June and August of 2008 and 2009 in Cahokia Creek, a small tributary of the Mississippi River in Illinois, along with a parallel study of Fundulus olivaceus between May and July of 2009 in Big Creek, a tributary of the Pascagoula River in Mississippi. Fish were recaptured approximately weekly, and habitat variables were measured. Estimated daily movement rates varied significantly both between locations and between years. Fundulus olivaceus in Big Creek moved <1 m per day, while F. notatus in Cahokia Creek in 2009 moved nearly 23 m per day. The distribution of movements was strongly leptokurtic in all three data sets. Differences in movement rates were attributed to significant differences in population size and habitat characteristics. Our data did not support the hypothesis that populations consist of distinct mobile and resident components. Instead, individual fish went through periods of little or no movement followed by extensive movement (consistent with the home range shift model of fish movement). We discuss the implications these results have for contact zone dynamics between these two species.