High Speed Rail (HSR) in Spain began in 1992 and curently has a network of about 3400 km. In this 25-year period, accessibility has progressively increased, and its spatial distribution has changed throughout the territory. This has had important implications for territorial cohesion, which is a strategic planning objective of transport infrastructures in the European Union. However, this increase in HSR has environmental impacts; among other effects, new transport infrastructures imply a loss of landscape structural connectivity. This paper has two objectives: to study the distribution and development of the changes across the territory produced by the arrival of HSR in Spain between 1990 and 2025, by looking at changes in potential accessibility and structural habitat connectivity at the national scale; and to study – at the same scale – the relationship between both variables through the cost of accessibility improvements (socioeconomic variable) in terms of the loss of structural connectivity (environmental variable). All the analyses were done using GIS-based indicators, reported in the literature to be useful at the Strategic Environmental Assessment (SEA) scale. The methodology is applied in different horizon years, namely 1990, 2007, 2016, and new proposed HSR lines to 2025 in Spain. The results show that throughout the whole period (1990−2025), accessibility improved by 74.7 % due to the extension of HSR. The most important period was 1990−2007, when the main socio-economic centres were connected by HSR, while connectivity, the environmental variable, declined by −3.4 %. The greatest connectivity loss was concentrated in 2007−2016, when the areas with the highest connectivity values in 1990 were the most affected. Our results show that a 1 % increase in accessibility implied a loss of connectivity of 0.03 % in the interval 1990−2007, while in the second period, the same 1 % increase entailed a 0.17 % loss; in the 2016−2025 scenario the value is intermediate (0.08). Our work contributes to adapting connectivity studies to the environmental assessment tiers in the transportation sector (i.e. plans, programmes and projects). Each stage has its limitations due to the lack of specific data or problems of spatial scale which must be publicly reported during environmental assessment processes. We also highlight the need for new research to establish a reliable spatial scale to assess the different effects of HSR corridors at the strategic level.