In this review we describe patterns and mechanisms by which habitat complexity is crucial for the functioning of 10 shallow lakes and ponds, and for the abundance and diversity of biological communities in these ecosystems. Habitat 11 complexity is affected by processes acting at different spatial scales, from the landscape scale to the ecosystem level 12 (i.e., morphometric attributes) generate different complexities, determining the potential for organisms to succeed and 13 processes to occur such as energy and nutrient transfer, fluxes of greenhouse gases, among others. At the local scale, the 14 three major habitats, pelagic, littoral, and benthic, are characterised by different degrees of structural complexity and a 15 particular set of organisms and processes. Direct and indirect effects of changes in within-lake habitat complexity can 16 either hinder or promote regime shifts in these systems. We also review several anthropogenic pressures 17 (eutrophication, urbanisation, introduction of exotic species, and climate change) that decrease lake resilience through 18 changes in habitat complexity and strategists for habitat complexity restoration. Overall, we emphasize the need to 19 preserve and restore habitat complexity as key challenges to account for ecosystem integrity, maintenance of 20 local/regional biodiversity, and provision of crucial ecosystem services (e.g., biodiversity, self-purification, and carbon 21 sequestration). European Union’s Horizon 2020- grant agreement No 869296 The PONDERFUL Project