The data set includes quantitative fish abundance counts estimated from video data files collected by a Dual-frequency IDentification SONar (DIDSON) placed at the junction of a water control structure located between Pool 2B and Crane Creek (41.62133N, -83.20769W) within Ottawa National Wildlife Refuge (Lucas County, Ohio). One-hour-long video data files were used to estimate fish activity in a restored coastal wetland within Ottawa National Wildlife Refuge in the Western Basin of Lake Erie. Over 800 video hours of fish movement were recorded at the fully open fish passage structure; 136 video data files were chosen at random to represent the full video data file set and are available upon request. Fish counts from the DIDSON video data files using four different methods are provided, comparing two semi-automated and two manual counting methods. Fish tracking software Echoview paired with an "Automod" script from Milne Technologies (Keene, Ontario, Canada) as well as DIDSON viewer software were used to semi-automate the fish counting process and estimate the total number of fish passing through the structure within a video hour. Manual counts were performed by individuals counting fish from video playback given a specific set of criteria to follow for either the full hour of playback or a set of three two-minute intervals. In addition to the count data, calculated values of percent differences are included offering a comparison of the semi-automated and manual count values. Environmental data (turbidity) associated with the time periods captured in the video data files are also included.