Large Language Models (LLMs) have made substantial progress in recent years, yet evaluating their capabilities in practical Retrieval-Augmented Generation (RAG) scenarios remains challenging. In practical applications, LLMs must demonstrate complex reasoning, refuse to answer appropriately, provide precise citations, and effectively understand document layout. These capabilities are crucial for advanced task handling, uncertainty awareness, maintaining reliability, and structural understanding. While some of the prior works address these aspects individually, there is a need for a unified framework that evaluates them collectively in practical RAG scenarios. To address this, we present CReSt (A Comprehensive Benchmark for Retrieval-Augmented Generation with Complex Reasoning over Structured Documents), a benchmark designed to assess these key dimensions holistically. CReSt comprises 2,245 human-annotated examples in English and Korean, designed to capture practical RAG scenarios that require complex reasoning over structured documents. It also introduces a tailored evaluation methodology to comprehensively assess model performance in these critical areas. Our evaluation shows that even advanced LLMs struggle to perform consistently across these dimensions, underscoring key areas for improvement. We release CReSt to support further research and the development of more robust RAG systems. The dataset and code are available at: https://github.com/UpstageAI/CReSt.