Hydromorphological alterations of the littoral zone of lakes may hinder the achievement of the environmental objective of the WFD, which is a good ecological status. We tested the HML- (HydroMorphology of Lakes) protocol which was designed for (i) the area-covering survey of littoral structures with a focus on anthropogenic modifications, and (ii) the planning of potential remediation. The degree of hydromorphological impact was assessed by an impact index in three littoral subzones, the sub-, eu- and epilittoral. In our study area, which comprised ten lakes, structural burdens came from (i) recreational activities, (ii) navigation facilities (including pleasure boating), and (iii) settlement. The epilittoral zone was generally the most affected, followed by the eulittoral and the sublittoral zone. The impact index of eulittoral subsegments was closely correlated to the index of the corresponding epilittoral subsegments. The HML protocol can also be applied to artificial and heavily modified lake water bodies (AWB, HMWB) that feature high proportions of quasi-natural objects. We concluded that the hydromorphological survey is an appropriate tool (i) for management and planning purposes of the responsible authorities, and (ii) to extrapolate results from very localised biotic samples into larger spacial dimensions (e.g. shore sections, lakes and lalceland areas).