As an essential component of global change, atmospheric nitrogen deposition exerts profound impacts on ecosystems. Since similar to 1900 AD, the rapid increase in global nitrogen deposition has become an environmental concern. Lakes, as key components of terrestrial ecosystems, warrant further investigation regarding their responses to atmospheric nitrogen deposition. Here, we selected lakes from the Loess Plateau and the arid Northwest China to examine their potential responses to atmospheric nitrogen deposition since similar to 1900 AD. Our results show that: (1) The persistently negative delta N-15 values in lake sediments from the Loess Plateau since the 1900s may be linked to enhanced atmospheric nitrogen deposition; (2) The responses from lakes in the arid Northwest China to atmospheric nitrogen deposition may occur decades later than the lakes in Loess Plateau; (3) Compared to the effects of atmospheric nitrogen deposition, human activities (such as road construction, agricultural practices) near or within the lake catchments have caused stronger variability in sedimentary delta N-15 values. Our findings indicate that gradual increases in atmospheric nitrogen deposition may lead to significant responses in lakes and a shift in nutrient limitation.