Urban freight distribution via inland waterways is an important way to boost the quality of life in major urban areas with dense water networks. Cost-effective autonomous pallet shuttle barges (PSBs) are key to accelerate the shift from road-based transport to inland waterways. Yet, the urban settings impede reliable centimeter-level localization at critical waterway sections. In this article, we propose a time-domain-optimized antenna array to provide high-precision 3-D localization in these complex environments with minimal shore-side infrastructure by exploiting impulse-radio ultra-wideband (IR-UWB) technology. To enable joint distance and 2-D angle-of-arrival (AoA) estimation, we present a novel IR-UWB antenna element that covers channels 5 and 7 of the IEEE 802.15.4z standard, serving as a building block for scalable multi-antenna systems. By leveraging the air-filled substrate-integrated-waveguide (AFSIW) technology and adopting a multi-objective system-level optimization strategy, excellent performance is reconciled with a compact footprint and cost-effective fabrication. The 3-D positioning accuracy of a 2 x 2 array is evaluated in stand-alone conditions and when installed on a metal plate mimicking a PSB's metal hull, showing that all distance errors and 97% of angular errors remain below 2 cm and 5 degrees, respectively. Finally, three anchor nodes, each consisting of a 1 x 4 array connected to a Pozyx hardware platform, are installed on a vessel navigating in a narrow canal below a bridge in Ghent. With only one shore-side UWB beacon node deployed, 96% of AoA estimation errors remain below 10 degrees, while the distance error remains below 10 cm, proving good installed performance in harsh urban shipping environments.