This survey aims to provide a comprehensive overview of the current research on underwater wireless sensor networks, focusing on the lower layers of the communication stack, and envisions future trends and challenges. It analyzes the current state-of-the-art on the physical, medium access control and routing layers. It summarizes their security threads and surveys the currently proposed studies. Current envisioned niches for further advances in underwater networks research range from efficient, low-power algorithms and modulations to intelligent, energy-aware routing and medium access control protocols.