Climate change is causing water temperature to rise, and many lakes in the boreal zone will experience browning of waters (brownification) due to increased input of dissolved organic carbon (DOC). In fish, warming may cause resource limitation and decrease both fish size and population abundance. Many fish species display ontogenetic niche shifts during their lifetime, shifting to larger prey as they grow. Brownification may change the timing for, the benefits from or prevent individuals from displaying ontogenetic niche shifts by decreasing large prey abundance in the benthic zone or making fast-moving prey harder to see. This can cause resource limitations, suppressing growth and population growth. This study investigated the effects of increasing DOC and water temperature on ontogenetic diet shifts, size structure, and population abundance in nine-spine stickleback (Pungitius pungitius) in an experimental pond system with a warming treatment and a gradient of DOC concentration. Warming had a negative effect on population number, biomass, maximum fish size, stomach fullness, and consumption of large prey. Contrary to expected outcomes, increasing DOC input resulted in higher population, biomass, and larger maximum sized fish as DOC increased. DOC did not negatively affect ontogenetic diet shifts. In the relatively shallow enclosures, the highest DOC concentration may not have reached the threshold where the shading effect of DOC overturns the benefits of extra nutrients associated with DOC. Hence, in shallow lake ecosystems, climate change induced DOC increase may support fish production, while warming may have strong negative effects on fish population abundance and size.