Although the initial inception, or genesis, of a city’s urban grid, is an important marker of its evolution over time, the process of urban transformation, or morphogenesis, can substantially alter its original townscape. This study sheds light on the morphogenetic impacts of the pre-industrialisation period on shaping the spatial configuration of the historical cores of three Dutch cities, Amsterdam, the Hague, and Delft. While some cities have undergone processes of expansion as physical growth of different grid types, others followed the historical patterns of genesis. This study aims to analyse the spatial mechanisms and morphological logic that lay out the medieval core of Dutch cities to create an adaptive approach for evolving in tandem with waterways. The study: i) reviews the literature and ongoing research initiatives on the Dutch urban planning paradigms and strategies through various time periods; ii) proposes a new spatio-temporal description of the medieval core of cities and their infrastructure, including streets and water networks; and iii) analyses the patterns of their historical core using a space syntax-based approach. Space syntax method and tools are applied to critically understand urban morphologies, as it provides quantitative analysis on multiple scales. The study shows how the relationship with water can constitute a path dependency for urban growth, highlighting the role of water in shaping movement patterns. Those different types of grid structures, such as organic, compact, accumulative, discontinuous, cellular etc., produce different spatial growth mechanisms as a powerful instrument in controlling and defining the functions of cities dominated by water.