Visual Language Models (VLMs) have become foundational models for document understanding tasks, widely used in the processing of complex multimodal documents across domains such as finance, law, and academia. However, documents often contain noise-like information, such as watermarks, which inevitably leads us to inquire: \emph{Do watermarks degrade the performance of VLMs in document understanding?} To address this, we propose a novel evaluation framework to investigate the effect of visible watermarks on VLMs performance. We takes into account various factors, including different types of document data, the positions of watermarks within documents and variations in watermark content. Our experimental results reveal that VLMs performance can be significantly compromised by watermarks, with performance drop rates reaching up to 36\%. We discover that \emph{scattered} watermarks cause stronger interference than centralized ones, and that \emph{semantic contents} in watermarks creates greater disruption than simple visual occlusion. Through attention mechanism analysis and embedding similarity examination, we find that the performance drops are mainly attributed to that watermarks 1) force widespread attention redistribution, and 2) alter semantic representation in the embedding space. Our research not only highlights significant challenges in deploying VLMs for document understanding, but also provides insights towards developing robust inference mechanisms on watermarked documents.