Implementing watershed management without considering all aspects may lead to instability, exacerbating unfavorable conditions. Adopting an integrated management approach is necessary for any watershed system. An important consideration in decision making and planning process is to quantify ecological impacts of management using landscape ecology framework. In this regard, uncertainty quantification is of great significance. This paper presents the concept of uncertainty and also the implication of uncertainty analysis for landscape ecology structure indices and also for weights assigned to the indices in a Multi-Criteria Decision Making (MCDM) technique in the Chehel-Chai Watershed. This watershed with an area of 256 km2 is located in the east of Golestan Province and in the upstream of the Gorganrood River Basin. The watershed is one of the most affected areas due to the land use change in the north of Iran. That is why it was chosen as the study the area. Based on the analysis, the highest and lowest uncertainty levels were identified for Edge Density (ED) and Riparian Proportion Index (RPI), respectively. In addition, the uncertainty analysis suggests that the weight assigned to Weighted Land Cover Area Index (WLCAI) has the highest uncertainty while the weight assigned to ED shows the lowest uncertainty. It is necessary to identify and quantify uncertainty so that more accurate and applicable inferences from research findings can be drawn.