Inland alkaline soda waters (ASW), such as Lake Neusiedl (LN), represent some of the most stable alkaline natural environments and unique ecosystems on Earth. Their European hotspot is located in Central Europe, where LN stands as the largest threatened representative, giving it practical importance. This study aims to compare fundamental hydro‐ecological variables of LN, including a habitat restoration site (LNres), with intermittent alkaline soda waters (IASW) in the adjacent subregion (Seewinkel). IASW serves as a characteristic close‐to‐nature reference status for natural ASW in order to restoration suggestions for LN. Variables investigated include depth, dissolved oxygen, pH, conductivity, algae‐free suspended solids, chromophoric dissolved organic matter and chlorophyll a. Significant differences were found among most variables between the three sites (Kruskal–Wallis ANOVA and Dunn's test), except for water depth, DO, conductivity, TSS‐Algfree and CHL between IASW and LNres, and CDOM between LNres and LN. Principal component analyses revealed that LNres is situated between LN (semi‐static) and reference IASW (astatic), supporting the hypothesis that LNres is closer to the reference IASW than the non‐restored part of LN. The hydro‐ecological properties of IASW and LNres are similar to the shallow shoreline of LN, suggesting that management strategies of intermittent waters can be applied to shoreline restoration of semi‐static waters. This can be achieved by restoring seasonal water dynamics and groundwater function through extensive wetland rehabilitation in the above‐ground and below‐ground watershed recharge area of LN. Additionally, extensive vegetation control (reed) should be implemented to prevent ASW from impacting the habitat and freshwater exchange.