Urbanization drives global CO2 levels higher, mainly due to human activities like fossil fuel combustion for heating, industry, and transportation. Emissions vary spatially based on factors like population density, land use or urban structure, underscoring the need to measure and understand local emissions to manage city-wide carbon budgets. The present study analyzes CO2, sensible and latent heat fluxes from two ICOS Associated eddy covariance flux towers in the city of Heraklion, Greece. Despite their proximity, only 1.5 km apart from each other, HECKOR and HECMAS represent distinct land use types: HECKOR is in the commercial city center, while HECMAS is in a residential area. Seasonal and diurnal CO2 flux patterns are therefore significantly different across the sites. HECKOR's fluxes align with commercial and working hours year-round, while HECMAS primarily captures CO2 emissions from residential heating during winter with only small fluxes during other times of the year. Furthermore, there is extreme directionality in CO2 fluxes measured in HECKOR, and thus the estimated diurnal patterns are affected by the seasonality of wind direction patterns. Dynamic flux footprints from both towers are analyzed to link observed CO2 fluxes to specific land use and land cover features. Additionally, we utilize the latest SUEWS CO2 modeling module, integrating TomTom traffic data and flux footprints to assess surface emissions alongside in-situ flux tower data. We also observe higher sensible heat fluxes in HECKOR, most probably due to higher building density and lower vegetation cover in the Heraklion central commercial district.