The native Yellowstone Cutthroat Trout (Oncorhynchus clarkii bouvieri Jordan and Gilbert, 1883) population in Yellowstone Lake, Yellowstone National Park, Wyoming, USA, is in decline because of competition from the introduced, invasive Lake Trout (Salvelinus namaycush Walbaum in Artedi, 1792). Gillnetting is used to suppress adult Lake Trout; however, methods are being developed to suppress embryos, including adding Lake Trout carcasses and carcass-analog pellets to spawning sites. Decomposing carcasses and analog pellets cause decreased dissolved oxygen concentrations thereby leading to Lake Trout embryo mortality, but the effects of these methods on primary producers are unknown. We deployed in-situ nutrient diffusing substrates (NDS) at 3 spawning sites. The 1^st site was treated with carcasses, the 2^nd site was treated with analog pellets, and a 3^rd lacked treatment (control). To estimate how suppression measures may alter nutrient limitation, we measured algal biomass in 6 NDS amendments at each site: nothing (control), N, P, N + P, ground carcasses, or pulverized analog pellets. We deployed 5 replicates of each amendment at each site before and after treating whole sites. N and P co-limited periphyton before carcasses or analog pellets were added to spawning sites (p < 0.01); however, nutrients were not limiting after the treatments were added to spawning sites (p = 0.31–1). Algal biomass was 4× higher after whole-site carcass treatments. In contrast, analog pellets appeared to suppress algal biomass in the amendments (20% of NDS at the control site post-treatment) and in the treatment plot (33% of pre-treatment biomass at analog pellet site). We also measured how individual ingredients in analog pellets altered periphyton biomass, which suggested that vitamin E, estrogen, and soybean oil ingredients reduced the growth of primary producers. Suppression methods may stimulate or reduce algal biomass, depending on the methods used, which could have cascading effects on food webs and potentially reduce the success of the control measures. Estimating how different Lake Trout suppression methods may alter basal resources in the littoral zone of Yellowstone Lake will help natural resource agencies develop effective plans to control invasive predators at early life stages while minimally altering ecosystems.