Increased phenotypic similarity between partners, termed assortative mating (AM), has been observed for many traits. However, it is currently unclear if these observations are due to mate choice for certain phenotypes, post-mating convergence, or a result of confounding factors such as shared environment or indirect assortment. To dissect these underlying phenomena, we applied Mendelian randomisation (MR) to 51,664 couples in the UK biobank to a panel of 118 phenotypes under AM. We found that 54% (64 of 118) of the tested traits had a causal relationship between partners, with female-to-male effects on average being larger. Forty traits, including systolic blood pressure, basal metabolic rate, weight and height, showed significantly larger phenotypic correlation than MR-estimates, suggesting the presence of confounders. Subsequent analyses revealed household income, overall health rating, education and tobacco smoking as major overall confounders, accounting for 29.8, 14.1, 11.6, and 4.78%, of cross-partner phenotypic correlations, respectively. We detected limited evidence for couple-correlation convergence (e.g. increased similarity with respect to smoking and medication use), measured by stratifying couples by their time spent together. Finally, mediation analysis revealed that the vast majority (>77%) of causal associations between one trait of an individual and a different trait of their partner is indirect. For example, the causal effect of the BMI of an individual on the overall health rating of their partner is entirely acting through the BMI of their partner. In summary, this study revealed many novel causal effects within couples, shedding light on the impact of confounding on couple phenotypic similarity.