The Sustainable Development Goals (SDGs) purport to report holistically on progress towards sustainability and do so using more than 231 discrete indicators, with a primary objective to achieve a balance between the environment, social and economic aspects of development. The research question underpinning the analyses presented in this paper is: are the indicators in the SDGs sufficient and fit for purpose to assess the trajectory of natural resources towards sustainability? We extracted the SDG indicators that monitor the state of natural resources, or alternately support policy or governance for their protection, and determined whether these are adequate to provide the essential data on natural resources to achieve the aims of the SDGs. The indicators are clustered into four natural resource categories—land, water (both marine and freshwater), air and biodiversity. Indicators for monitoring land resources show that the most comprehensive land resource indicator for degraded land is not fully implemented and that missing from land monitoring is an evaluation of vegetation health outside of forests and mountains, the condition of soils, and most importantly the overall health of terrestrial ecosystems. Indicators for monitoring water resources have substantial gaps, unable to properly monitor water quality, water stress, many aspects of marine resources and, most significantly, the health of fresh and salt water ecosystems. Indicators for monitoring of air have recently become more comprehensive, but linkage to IPCC results would benefit both programs. Monitoring of biodiversity is perhaps the greatest weakness of the SDG Agenda, having no comprehensive assessment even though narrow aspects are monitored. Again, deliberate linkages to other global biodiversity programs (e.g., CBD and the Post-2020 Biodiversity Framework, IPBES, and Living Planet) are recommended on condition that data can be defined at a country level. While the SDG list of indicators in support of natural resource is moderately comprehensive, it lacks holistic monitoring in relation to evaluation of ecosystems and biodiversity to the extent that these missing but vital measures of sustainability threaten the entire SDG Agenda. In addition, an emerging issue is that even where there are appropriate indicators, the amount of country-level data remains inadequate to fully evaluate sustainability. This signals the delicate balance between the extent and complexity of the SDG Agenda and uptake at a country level.