In this work, we proposed to include remote sensing techniques as a part of the methodology for natural lake bottom mapping, with a focus on the littoral zone. Due to the inaccessibility of this zone caused by dense vegetation, measurements of the lake bottom and the coastline are also difficult to perform using traditional methods. The authors of this paper present, discuss and verify the applicability of remote sensing active sensors as a tool for measurements in the shore zone of a lake. The single-beam Lowrance HDS-7 ComboGPS echosounder with an 83/200 kHz transducer and a two-beam LiDAR RIEGL VQ-1560i-DW scanner have been used for reservoir bottom measurements of two neighboring lakes, which differ in terms of water transparency. The research has found a strong correlation between both sonar and LiDAR for mapping the bottom depth in a range up to 1.6 m, and allowed LiDAR mapping of approximately 20% of the highly transparent lake, but it has not been found to be useful in water with low transparency. In the light of the conducted research, both devices, sonar and LiDAR, have potential for complementary use by fusing both methods: the sonar for mapping of the sublittoral and the pelagic zone, and the LiDAR for mapping of the littoral zone, overcoming limitation related to vegetation in the lake shore zone.