Convolutional Neural Networks (CNN) consist of various hyper-parameters which need to be specified or can be altered when defining a deep learning architecture. There are numerous studies which have tested different types of networks (e.g. U-Net, DeepLabv3+) or created new architectures, benchmarked against well-known test datasets. However, there is a lack of real-world mapping applications demonstrating the effects of changing network hyper-parameters on model performance for land use and land cover (LULC) semantic segmentation. In this paper, we analysed the effects on training time and classification accuracy by altering parameters such as the number of initial convolutional filters, kernel size, network depth, kernel initialiser and activation functions, loss and loss optimiser functions, and learning rate. We achieved this using a well-known top performing architecture, the U-Net, in conjunction with LULC training data and two multispectral aerial images from North Queensland, Australia. A 2018 image was used to train and test CNN models with different parameters and a 2015 image was used for assessing the optimised parameters. We found more complex models with a larger number of filters and larger kernel size produce classifications of higher accuracy but take longer to train. Using an accuracy-time ranking formula, we found using 56 initial filters with kernel size of 5 × 5 provide the best compromise between training time and accuracy. When fully training a model using these parameters and testing on the 2015 image, we achieved a kappa score of 0.84. This compares to the original U-Net parameters which achieved a kappa score of 0.73.