A significant change to the land cover in the Hula Valley was carried out during the 1950s: A swampy area densely covered by aquatic vegetation and the old shallow lake Hula were drained. The natural shallow lake and swamps land cover were converted into agricultural development land use in two stages: (1) Drainage that was accomplished in 1957; (2) Implementation of the renovated hydrological system structure, including the newly created shallow Lake Agmon-Hula (LAH), was completed in 2007. The long-term data record of the restored diversity of the submerged and emerged aquatic plant community, and its relation to water quality in the newly created shallow Lake Agmon-Hula LAH, was statistically evaluated. Internal interactions within the LAH ecosystem between aquatic plants and water quality, including nitrification, de-nitrification, sedimentation, photosynthetic intensity, and plant biomass and nutrient composition, were statistically evaluated. The plant community in LAH maintains a seasonal growth cycle of onset during late spring–summer and dieback accompanied by decomposed degradation during fall–early winter. The summer peak of aquatic plant biomass and consequent enhancement of photosynthetic intensity induces a pH increase during daytime and carbonate precipitation. Nevertheless, the ecosystem is aerobic and sulfate reduction and H2S concentration are negligible. The Hula reclamation project (HP) is aimed at the improvement of eco-tourism’s integration into management design. The vegetation research confirms habitat enrichment.