As the world explores opportunities to develop offshore renewable energy capacity, there will be a growing need for pre-construction biological surveys and post-construction monitoring in the challenging marine environment. Underwater video is a powerful tool to facilitate such surveys, but the interpretation of the imagery is costly and time-consuming. Emerging technologies have improved automated analysis of underwater video, but these technologies are not yet accurate or accessible enough for widespread adoption in the scientific community or industries that might benefit from these tools. To address these challenges, prior research developed a website that allows to: (1) Quickly play and annotate underwater videos, (2) Create a short tracking video for each annotation that shows how an annotated concept moves in time, (3) Verify the accuracy of existing annotations and tracking videos, (4) Create a neural network model from existing annotations, and (5) Automatically annotate unwatched videos using a model that was previously created. It uses both validated and unvalidated annotations and automatically generated annotations from trackings to count the number of Rathbunaster californicus (starfish) and Strongylocentrotus fragilis (sea urchin) with count accuracy of 97% and 99%, respectively, and F1 score accuracy of 0.90 and 0.81, respectively. The thesis explores several improvements to the model above. First, a method to sync JavaScript video frames to a stable Python environment. Second, reinforcement training using marine biology experts and the verification feature. Finally, a hierarchical method that allows the model to combine predictions of related concepts. On average, this method improved the F1 scores from 0.42 to 0.45 (a relative increase of 7%) and count accuracy from 58% to 69% (a relative increase of 19%) for the concepts Umbellula Lindahli and Funiculina.