The bursty many-to-one communication pattern, typical for data acquisition systems, is particularly demanding for commodity TCP/IP and Ethernet technologies. The problem arising from this pattern is widely known in the literature as incast and can be observed as TCP throughput collapse. It is a result of overloading the switch buffers, when a specific node in a network requests data from multiple sources. This will become even more demanding for future upgrades of the experiments at the Large Hadron Collider at CERN. It is questionable whether commodity TCP/IP and Ethernet technologies in their current form will be still able to effectively adapt to bursty traffic without losing packets due to the scarcity of buffers in the networking hardware. This thesis provides an analysis of TCP/IP performance in data acquisition networks and presents a novel approach to incast congestion in these networks based on software-based packet forwarding. Our first contribution lies in confirming the strong analogies between the TCP behaviour in data acquisition and datacenter networks. We also provide experimental evaluation of different proposals from the datacenter environment for application in data acquisition to improve performance and reduce buffer requirements. The second contribution lies in the design and experimental evaluation of a data acquisition network that is based on software switches. Performance has traditionally been the challenge of this approach, but this situation changes with modern server platforms. High performance load balancers, proxies, virtual switches and other network functions can be now implemented in software and not limited to specialised commercial hardware, thus reducing cost and increasing the flexibility. We first design and optimise a software-based switch with a dedicated, throughput-oriented buffering mechanism for data acquisition. Our experimental results indicate that it performs significantly better than some typical Ethernet switches under heavy congestion. The optimised software switch with large packet buffer reaches maximum bandwidth and completely avoids throughput degradation typical for hardware switches that suffer from high packet drop counts. Furthermore, we evaluate the scalability of the system when building a larger topology of interconnected software switches. We highlight aspects such as management, costs, port density, load balancing, and failover. In this context, we discuss the usability of software-defined networking technologies, Open vSwitch Database and OpenFlow, to centrally manage and optimise a data acquisition network. We have built an IP-only parallel leaf-spine network consisting of eight software switches running on separate physical servers as a demonstrator.