One of the most significant threats to Lake Titicaca is pollution, primarily from agricultural runoff, and wastewater contaminated with lead and mercury from heavy metal mining. Increased urbanization and industrial activities around the lake have contributed to the degradation of water quality, threatening the survival of aquatic life, such as the critically endangered giant Titicaca water frog, and impacting the health of local communities that rely on the lake for their water supply.
Non-native species, such as the water hyacinth, and introduced fish species like trout, have had a negative impact on the native biodiversity of Lake Titicaca. These invasive species disrupt the natural balance of the ecosystem and threaten the survival of indigenous fish species, such as Andes ispi, karachi, humanto, and boga carps.
The effects of climate change, such as rising temperatures, altered precipitation patterns, and glacial melting, pose a significant threat to Lake Titicaca. The effects of climate change have drastically altered the water levels, pushing species to migrate to deeper regions. The high-altitude environment of the lake makes it of significant interest to climate change researchers, as its sensitive ecosystems act as an early-warning indicator of global warming's broader effects.
Overfishing as a result of development in Lake Titicaca has decimated some of the region’s key native fish populations. Of particular note: stocks of karachi, a tiny species that local groups have subsisted on since pre-Incan times, have been severely impacted due to unregulated fishing practices.