Some of Fishing Creek is stocked by the Fishing Creek Sportsman's Association and contains populations of brook trout, rainbow trout, and brown trout. Many of them are sizable; the largest one caught in Fishing Creek weighed and was long. All streams in the watershed are suitable for trout habitation according to the Pennsylvania Fish and Boat Commission. An 1887 book stated that Fishing Creek and its tributaries may have once been "alive with trout". In the upper part of the watershed, wild brook trout are most common in West Branch Fishing Creek and fish in general are least common in East Branch Fishing Creek. West Creek has higher fish diversity than any other stream in the upper part of the watershed and is also the only place that is inhabited by wild brown trout. In addition, sculpin and cutlips minnow have been observed in large numbers in the creek and its tributaries. Less commonly observed fish in the upper part of the watershed include johnny darters, white suckers, and black-nosed dace. It is difficult for fish to spawn in the creek because of poor water quality near Benton, a lack of food, and dry headwaters for part of the year. The fish diversity in East Branch Fishing Creek and West Branch Fishing Creek is also significantly affected by episodic acidification, which is caused by acid rain falling in areas with no limestone in the bedrock. The main stem experiences similar problems but to a lesser extent, and the tributaries Coles Creek and West Creek experience the problems even less.
