Human-induced pressures that are closely associated with the loss of natural habitats and overall habitat degradation of littoral habitats are threatening lakes and their ecological integrity globally. Therefore, creating littoral habitats in lake systems to enhance habitat complexity and heterogeneity seems a suitable method to stimulate the production of higher trophic levels by improving primary and secondary production. However, the local climate conditions and management practices could reshape the physical and chemical characteristics of these newly created littoral habitats, thereby affecting the primary and secondary production that forms the base of the food web, ultimately making it difficult to predict the response of higher trophic levels to these newly created littoral habitats. Here, we studied how local climate conditions and management practices reshape the characteristics of the newly created littoral habitats in a wind-exposure lake on various ecosystem parameters including sediment properties, nutrient availability, primary producers, and invertebrates in the newly created archipelago Marker Wadden in Lake Markermeer, The Netherlands. To this end, we selected engineered littoral habitats varying in climate conditions and building sediments, which resulted in 3 types of littoral habitats: (1) fully exposed to wind, (2) semi-sheltered, and (3) fully-sheltered from wind effects. We found that the physical parameters (including water depth, temperature, suspended solids concentrations, and conductivity) significantly differed among sites. The nutrients in the water (including total nitrogen, total phosphorus, particulate organic phosphorous, dissolved inorganic phosphorus, nitrate, and ammonium) also significantly differed among sites. Meanwhile, the organic contents in the sediment showed an increasing trend while fetch length showed a reverse trend when moving from the Exposure site to the Fully sheltered site, although they are not statistically different. Primary producers were present as benthic algae, periphyton and submerged macrophytes, with significantly higher biomass (algae) and cover (macrophytes) in the sheltered sites compared to the exposed sites. Furthermore, we found that total benthic fauna density, total cladocerans density, and total rotifer density and their community compositions significantly differed among sites. These results suggest enhancing habitat complexity and heterogeneity through littoral habitat creation could be used to stimulate the recovery of higher trophic level production, which in turn improves lake ecological integrity.